- Chimera-users - RBVI Mailing Lists

Color-picker/eye-dropper tool?
by Oliver Clarke 30 Oct '14

30 Oct '14

Greetings, Just a request for the wish-list - is there any prospect of implementing a color-picker (eye-dropper) in chimera at some point? This would be particularly handy for matching colors between figures, or to figures made in another program. At the moment I use an external mac app, Sip, to do do the same thing, but an integrated tool would be nice to have. Best, Oliver.

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change segmented object colour
by Deran Reddy 29 Oct '14

29 Oct '14

Dear Sir/Madam Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. Any help would be greatly appreciated. Kind Regards Deran Reddy <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table>

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DLP-link for 3D sequential stereo viewing
by David Bhella 29 Oct '14

29 Oct '14

Dear colleagues, I am having some difficulty configuring a 3D projector for use with chimera, so I am hoping that someone may be able to offer some advice. Briefly we have a Projection Design F35 DLP projector that uses DLP-link to synchronise the shutter glasses. I have a Windows 7 PC with an nVidia K-series video card to run the projector (I have to use Windows - please don’t say use linux!). Through the nVidia GUI I set the driver to DLP, but in chimera the image does not seem to be flickering and there is no 3D image, even though the glasses are shuttering. The image is distorted in a similar way to that seen with shutter glasses but it is static. The only way I can get chimera to give a flickering image is when I set it to use the DIN socket, but of course the image is not synched to the glasses. I would be grateful for any advice on system settings I may need to make to get this working. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Applying settings from one molecule to another
by Oliver Clarke 28 Oct '14

28 Oct '14

Hi, Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? I’ thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. Best, Oliver.

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fiting onto density map
by Urszula Uciechowska 28 Oct '14

28 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Does anyone can help me here? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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visualising electron density map
by Neha Gandhi 28 Oct '14

28 Oct '14

Dear Support, I have downloaded pdb file 3j5r and also downloaded corresponding electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777) The microscopy structure was done in presence of the ligand and the original paper reports electron density for the ligand (Extended figure 7 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html) However, the authors couldn't model the orientation of ligand in the binding site. I have docked the ligand in the binding site and I am trying to visualize if the docked ligand fits well in the electron density or not. Is there a way to visualise the electron density only for the ligand in UCSF chimera as reported in the above nature paper? Thank you for kind attention, Awaiting your reply, Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] aligning PDB file
by Eric Pettersen 27 Oct '14

27 Oct '14

openModels.list doesn't necessarily return the currently open models in any particular order. The if/else part of the code is testing whether the first model in the model list has model ID 0. If it does then it assigns the first model to m0 and the second model to m1. Otherwise, it makes the reverse assignment -- so m0 will always contain model 0 (the code assumes there are only two models open). As per the example in that mail, chain A of model 0 had been superimposed on chain B of model 1. That's why the "chains" were set to "[m0.sequence('A'), m1.sequence('B')]" for handing off to makeAlignment -- those were the chains desired in the alignment. Are you saying you don't know which chain from each PDB file to use? How do you know which to superimpose then? --Eric On Oct 27, 2014, at 4:05 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > Thank you Eric for the URL. > Could you please help me understand what is going on here? > from chimera import openModels, Molecule # import > > models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs > > if models[0].id == 0: # what does this do? > m0, m1 = models > > else: # > m1, m0 = models # why interchanged the m1, mo? > chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? > > > > > > > On Monday, October 27, 2014 6:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Hi Sanjeev, > Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > >> Hi Chimera Developers, >> >> I've used chimera mostly by GUI inerface [click]. >> How do I get the match-align work from command line in a python script? >> I read a good description at: >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html >> >> work flow of the script is: >> take in 2 pdb files and match->align them. >> >> I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? >> >> How do I get the output saved in a FASTA file without MAV interface? >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > >

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aligning PDB file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? How do I get the output saved in a FASTA file without MAV interface?

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fiting onto density map
by Urszula Uciechowska 27 Oct '14

27 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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Double structure while loading the pdb file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Members/Developers, I loaded pdb file 1U19- Bovine Rhodopsin. structure is double the length what is to be. On terminal, on doing color red: 113 I see that 2 residues are colored. Why there are 2 molecules in same file? How do I hide one molecule?

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CASTp
by George Tzotzos 24 Oct '14

24 Oct '14

I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards George

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Combine maps
by Jian Guan 24 Oct '14

24 Oct '14

Hi all, Can I combine two mrc maps into one? And the two maps are with different pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two into one with pixel size of 2.33 A. I tried segmentation, and made two maps. But I failed to combine them. Can anybody help me for that? Thanks. Sincerely yours, Jian

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change size of a shape
by Jean-Didier Maréchal 22 Oct '14

22 Oct '14

Dear all, I would like to animate a sphere that grows. But I could alter the dimension of an object created with the shape command? thank you JD

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question
by JESSE JAYNES 22 Oct '14

22 Oct '14

Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse

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display ribbon for CA atoms
by Bala subramanian 21 Oct '14

21 Oct '14

Friends, I am trying to visualize a helical structure containing only the CA atoms. Chimera doesnt display ribbon for some of atoms, a reason which i dnt understand. I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am pasting the coordinates below of my pdb. You insights would be of great help to resolve the problem. MODEL 1 ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 END -- C. Balasubramanian

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Ellipsoid using chimera
by Anu Chandran 21 Oct '14

21 Oct '14

Dear users, I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? Thanking you, with regards, Anu

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Re: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 16 Oct '14

16 Oct '14

Dear Dr. Elaine & Rama The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 11:34 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Wednesday, October 15, 2014 9:34:43 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: How to display H-bonds between atoms of > selected residues ? > > Dear Mahendra, > First, you would select residue 291. There are many ways to select. One > way is to Ctrl-click to select some atom or bond in that residue and then > press up arrow on your keyboard one time to select the whole residue. > Another way is to show Sequence (menu Favorites… Sequence) and drag a box > on just that residue in the sequence, which will select it in the structure. > > Then if you are using the FindHBond dialog (in menu under Tools… Structure > Analysis), there is an option in dialog that you need to turn on, "Only > find H-bonds", with additional choices: > with at least one end selected > with exactly one end selected > with both ends selected > between selection and atom spec… > > You can click the Help button on FindHBond to see the full manual page. > > If you are using the "findhbond" command, there is a "selRestrict" option > to do the same things. Use command "help findhbond" to see the possible > values of that option. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Oct 15, 2014, at 8:09 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > > Hi, Rama > > > > I tried by selecting the residue, but still all hydrogen > bonds were displayed as before. I just want to display H-bonds related with > the residue only. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati,OH > > > > > > On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > From: rama david > > Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Subject: Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > > > Dear Sir, > > You first select the residue and then go in structure analysis tools > > I think this should work fine. If this not work then let it know > please > > > > best wishes, > > > > > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > > Dear Chimera Users, > > > > By using 'Structure analysis tool' of Chimera, all possible > H-bonds between atoms were displayed. > > > > I am interested to display only H-bonds between atoms of > selected residues, say H-bonds between atoms of residue number 291 and > atoms of rest of the residues including atoms of residue 291 in a pdb file > with 300 residues. Any suggestion definitely helps me a lot. > > > > Thank you, > > Mahendra Thapa > > University of Cincinnati,OH > >

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Dim colors in Chimera on OS X 10.10 public beta (Yosemite)
by Jethro Hemmann 16 Oct '14

16 Oct '14

Hi, I'm currently using Chimera on my Macbook running the public beta of Yosemite. The colors of the molecules appear very dim and they are hard to recognize, as can be seen in the attached screenshot. In this example, the lipid chains are colored orange, while the water molecules should by cyan. The colors in the menu Actions --> Color seem to appear with their correct brightness, although. I also tried the daily build of the alpha version of Chimera, but the problem persists. Is this problem related to Yosemite? Or do I have to adjust some settings? Thanks a lot, Jethro

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Ligand selection information
by Korbin West 15 Oct '14

15 Oct '14

Hello. I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. Here's what I have at the moment, writing the information to a file. runCommand('open 2izh') runCommand('sel ligand') runCommand("writesel ~/Desktop/testligand.txt") And here's an excerpt of the testligand.txt file: #1 BTN 300.B #1 HOH 1777.B #1 HOH 1778.B #1 BTN 300.D #2 ACY 801.B #2 SER 308.C #3 BTN 300.B Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. Thanks so much, Korbin West

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Re: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 15 Oct '14

15 Oct '14

Hi, Rama I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* rama david > *Sent:* Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central > America > *To:* Thapa, Mahendra (thapamb) > *Subject:* Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > Dear Sir, > You first select the residue and then go in structure analysis tools > I think this should work fine. If this not work then let it know please > > best wishes, > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > >> Dear Chimera Users, >> >> By using 'Structure analysis tool' of Chimera, all possible >> H-bonds between atoms were displayed. >> >> I am interested to display only H-bonds between atoms of >> selected residues, say H-bonds between atoms of residue number 291 and >> atoms of rest of the residues including atoms of residue 291 in a pdb file >> with 300 residues. Any suggestion definitely helps me a lot. >> >> Thank you, >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 14 Oct '14

14 Oct '14

Dear Chimera Users, By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed. I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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co-factor FAD in autodock-vina
by 宋青 14 Oct '14

14 Oct '14

Dear Chimera Design Team, We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497

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Mutations or residue selections
by Susan Cotmore 13 Oct '14

13 Oct '14

Hi, Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain? Is it possible to model potential effects of introducing specific mutations? Many thanks, Susan Cotmore

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Question about unit of electron density
by Matthias Fellner 13 Oct '14

13 Oct '14

Dear Elaine Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know. So I wanted to wait for my thanks to see if I can ask another question right away: What unit do I report for the "level" of a shown electron density map. I assume it is σ (lower case letter sigma) for example 1.2σ? I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check. Thank you Matthias Fellner ________________________________________ From: Elaine Meng [meng(a)cgl.ucsf.edu] Sent: 04 October 2014 06:50 To: Matthias Fellner Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Question about RMSD calculation of MatchMaker Hi Matthias! As shown in your image of the dialog, you’re using the “Iterate by pruning…” option that removes farther-apart pairs from the fit. That’s why you could get different numbers of pairs used to calculate the RMSD even if all chains contain the same numbers of residues. Iteration is described in the MatchMaker docs: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> If you turn off the “iterate” option, it will not try to improve the fit by pruning and will instead use all the pairs (CA-CA atom pairs of residues aligned in the sequence alignment). If the structures include the same residues for each chain, the pairwise chain-chain RMSDs will all be calculated from the same number of CA-CA atom pairs. The dialog image also shows you are fitting A-B, A-C, A-D. For completeness you may also want to try B-C, B-D, C-D. Another issue is that MatchMaker or its command equivalents (mmaker, matchmaker) only use one atom per residue, CA, and only considers aligned biopolymer chains (peptides, nucleic acids). If that’s what you want, no worries. However, you could use the “match” command instead and specify any sets of atoms for RMSD calculations, such as all backbone, with or without iteration. However, it’s harder to use since you have to specify the atoms in the command line yourself, unlike MatchMaker that figures out which atoms to pair automatically. You could include waters, but it would be tedious/difficult to specify each water residue by name, in the corresponding orders, for the two structures to be matched. Also the waters would have to be in the respective models. Matchmaker vs. match is discussed in the following link: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> “match” command manpage, examples: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> another “match” example in a tutorial, see the Matching section in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> If you are interested in the variation over the length of the chain as opposed to getting a single number, a nice way to show that is to first superimpose the chains, then associate them all with a single copy of the sequence. Then over the sequence you can display an RMSD histogram showing the alpha-carbon (or other atoms, depending on which RMSD you choose) structural variability at each position in the sequence. To do that: (1) superimpose chains however you like (Matchmaker or match) (2) show sequence of any one of them, presumably they are basically the same (menu: Favorites… Sequence, choose one) (3) in the sequence window, use Structure… Associations to associate all copies of the structure with the single sequence (4) in the sequence window, use the Headers menu to show the RMSD of interest (and hide other headers you don’t want to see) You can even show these RMSD values with colors or worm thickness on one of the copies, as described in more detail here: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009710.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 1, 2014, at 9:38 PM, Matthias Fellner <mfellner(a)chemistry.otago.ac.nz> wrote: > Good day > > I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. > A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. > > I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). > > The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. > > I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. > > Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. > > In addition a small question which I guess wont be possible – is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? > > Thank you > Matthias > > > <image001.png> > > Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 191 atom pairs is 0.506 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 188 atom pairs is 0.551 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 193 atom pairs is 0.336 angstroms > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Measuring volume inside virus caspid
by Tom Goddard 13 Oct '14

13 Oct '14

Hi Reggie, I measure the volume inside the capsid of bacteriophage P22 from Electron Microscopy Databank entry 1220 as about 77,000 cubic nanometers. Here’s how I calculated it in Chimera. The idea is to fit a surface that is something between an icosahedron and a sphere to the inside of the capsid then measure the volume within that surface. The Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) can make this surface. But the problem is that the EMD 1220 density map is not in a standard icosahedral orientation. The closest orientation is 2-fold symmetry axis along x, 3-fold symmetry axis along z (called 2n3r in Chimera). That orientation looks to be about 5 degrees out of alignment with the virus. So I set the radius to 320 (about the size of the capsid), sphere factor to 0.5 to approximate the spherical shape of the virus, and subdivision factor to 100. Then I created a density map that is ones inside this surface and zeros outside with the command “mask ones #1” (the icosahedron surface is model #1, as shown in the Model Panel dialog, Favorites menu). Then I fit this icosahedron map to EMD 1220 to get the correct alignment using the Fit in Map tool (menu Tools / Volume Data / Fit in Map, fit #2 in #0). I judge the fit is good by seeing that the virus capsid proteins stick out uniformly from the surface of the fit mask map. Then I align the original icosahedron surface to the fit mask using “matrixcopy #1 #2”. Then I adjust the icosahedron surface radius and sphere factor (285 and 0.54) to visually match the inner boundary of the EMD 1220 capsid. To see that I clip the EMD 1220 map in half using Per-Model Clipping (menu Tools / Depiction). Then I measure the enclosed volume of that aligned icosahedron surface using the Measure Volume and Area tool (menu Tools / Volume Data), and I get 77 million cubic Angstroms, or 77,000 cubic nanometers. See attached picture with aligned icosahedron surface shown transparent and brown. Tom On Oct 13, 2014, at 10:40 AM, Reginald McNulty wrote: > Hi Tom, > Can you tell me the tricks of how to calculate the volume of just the interior for EMD-1220? > Reggie > > On Oct 9, 2014, at 5:58 PM, Tom Goddard wrote: > >> Hi Reggie, >> >> What are you trying to calculate? Chimera can calculate the volume inside your density map surface if that is what you want. If it is just a capsid map then it won’t include the hollow interior. There are tricks to include the interior. If you really care about icosahedron volumes Chimera gives the exact value by summing polyhedral volumes. The Chimera icosahedron radius is the distance from the center to a vertex. The measure volume command reports the enclosed volume of the icosahedron with its flat faces as 58.7e6 for radius 285. As you note a sphere of radius 285 has volume 95e6. >> >> Tom >> >> >> On Oct 9, 2014, at 5:34 PM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> Eager to hear your thoughts on what’s below. >>> >>> I’ve done the math by hand for how to calculate the volume of an icosahedron. One of them (exsphere) gives the exact answer shown in Chimera with 'measure volume'. I’ll give a brief definition below and then show all calculations. The volume (V) of an icosahedron depends on the length of the edge (distance between five folds). My understanding is that there are different ways of drawing the radius (R) to calculate the length of an edge (a). Assuming an exsphere radius of 285 angstroms, I can calculate a volume of 58709669.80741614 cubic angstroms (or 59 million cubic angstroms) which is exactly the answer shown in chimera. However, I suspect the midsphere radius of 285 angstroms, yielding a volume of 95379640.39879936 cubic angstroms (or 95 million cubic angstroms) is a closer approximation, as this answer is very close to that obtained assuming V=4/3*(pi)*r^3 (97 million cubic angstroms). >>> >>> Definitions: >>> Inscribed sphere: http://en.wikipedia.org/wiki/Inscribed_sphere >>> Midsphere: http://en.wikipedia.org/wiki/Midsphere >>> exsphere: http://en.wikipedia.org/wiki/Exsphere_(polyhedra) >>> >>> Useful online calculator: http://calcverter.blogspot.com/2014/08/icosahedron-edge-area-volume-exspher… >>> >>> Assuming a radius of 285 angstroms, here are the calculations for volume 3 different ways: >>> >>> Method A >>> R(m)- Midsphere radius= 285 Å >>> >>> R(m)=a / 4 * ( 1 + √5 ) >>> --------------------------------------- >>> multiply both sides by 4 >>> --------------------------------------- >>> 285(4)= a(1+√5) >>> = a(3.23606797749979) >>> ---------------------------------------- >>> a=285(4)/3.23606797749979 >>> ---------------------------------------- >>> a=352.27937358744003 >>> ---------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> >>> = 5/12 * 43718136.95711854 *(3 + √5) >>> = 5/12 *43718136.95711854 5.23606797749979 >>> =95379640.39879936 >>> --------------------------------- >>> or 95 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method B >>> R(e)- Exsphere radius- 285 >>> >>> R(e) = a / 4 * √(10 + 2 * √5) >>> ---------------------------------- >>> writing in python was easier for me here: >>> >>> 285=a/4 * math.sqrt(10+2*math.sqrt(5)) >>> 285=a/4 * 3.804226065180614 >>> ---------------------------------------------- >>> >>> solve for a: >>> a=(285/ 3.804226065180614)*4 >>> a=299.6667339079062 >>> >>> -------------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> -------------------------------------------------- >>> writing in python is a little easier here: >>> >>> V= ((5/12.0)*(299.6667339079062**3)*(3+math.sqrt(5))) >>> >>> = 58709669.80741614 >>> -------------------------------- >>> or 58 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method C >>> R(i)- Insphere radius (tangent to face of icosahedran) >>> >>> R(i) = a / 12 * √3 * ( 3 + √5 ) >>> >>> ----------------------------- >>> >>> 285 = a/12 *((math.sqrt(3))*(3+math.sqrt(5))) >>> >>> 285= a/12 * 9.069135768914048 >>> >>> a= (285/9.069135768914048)*12 >>> = 377.1031868022763 >>> ---------------------------------------- >>> >>> Use edge of 377.1031868022763 to calculate volume >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> ------------------------------------------- >>> >>> V= ((5/12.0)*(377.1031868022763**3)*(3+math.sqrt(5))) >>> V= 116996977.425189 >>> --------------------------------------------- >>> >>> or 116 million cubic Å >>> >>> ------------------------------------------ >>> >>> Reggie McNulty >>> >>> On Oct 9, 2014, at 4:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>>> When you use the “measure volume” command on an icosahedral cage it is measuring the volume enclosed in the polygonal solid defined by the cage, not the volume of a sphere. I don’t know what you mean by “exsphere”, “midsphere”, “calculate by hand”. >>>> >>>> Tom >>>> >>>> >>>> On Oct 9, 2014, at 1:01 PM, Reginald McNulty wrote: >>>> >>>>> I manually fixed the cage and shrunk it to encompass the internal DNA using a radius of 285. I used the measure volume command to measure the volume inside the cage. Can Chimera show sphere it is using to calculate calculate the volume? A cage with radius 285 angstroms gives a volume of 58 million cubic angstroms. By hand, I can calculate volume of also 58 million cubic angstroms using an exsphere radius of 285; edge is 300 angstroms. However, a midsphere radius of 285 gives me an edge of 352 angstroms and volume of 95 million cubic angstroms. >>>>> Reggie >>>>> >>>>> On Oct 8, 2014, at 2:24 PM, Tom Goddard wrote: >>>>> >>>>>> Yes you could probably fix the alignment of a cage by hand in Chimera so it looked decent. If you want to do some analysis using the symmetry that is harder. >>>>>> >>>>>> Tom >>>>>> >>>>>> On Oct 8, 2014, at 2:14 PM, Reginald McNulty wrote: >>>>>> >>>>>>> Never mind. I think it’s close enough with 2fold on x, 3 fold on z, with extra rotation. >>>>>>> On Oct 8, 2014, at 2:07 PM, REGINALD MCNULTY wrote: >>>>>>> >>>>>>>> Thanks. It works. >>>>>>>> I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? >>>>>>>> Reggie >>>>>>>> On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: >>>>>>>> >>>>>>>>> Hi Reggie, >>>>>>>>> >>>>>>>>> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >>>>>>>>> >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> open 2xyz >>>>>>>>> rainbow chain >>>>>>>>> sym #0 surf true >>>>>>>>> >>>>>>>>> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >>>>>>>>> >>>>>>>>> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >>>>>>>>> molmap #0 10 sym i,n25r >>>>>>>>> >>>>>>>>> >>>>>>>>> <2xyz.jpg> >>>>>>>>> >>>>>>>>> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >>>>>>>>> >>>>>>>>>> Dear Tom, >>>>>>>>>> >>>>>>>>>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>>>>>>>>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>>>>>>>>> >>>>>>>>>> All the best, >>>>>>>>>> -Reggie >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reginald McNulty, Ph.D. >>>>>>>>>> Postdoctoral Research Associate >>>>>>>>>> The Scripps Research Institute >>>>>>>>>> Johnson Lab >>>>>>>>>> Department of Integrative Structural and Computational Biology >>>>>>>>>> 10550, N. Torrey Pines Road, MB-31 >>>>>>>>>> La Jolla, California 92037 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> All the best, >>>>> -Reggie >>>>> >>>>> -- >>>>> Reginald McNulty, Ph.D. >>>>> Postdoctoral Research Associate >>>>> The Scripps Research Institute >>>>> Johnson Lab >>>>> Department of Integrative Structural and Computational Biology >>>>> 10550, N. Torrey Pines Road, MB-31 >>>>> La Jolla, California 92037 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >> > >

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